Nanoindentation of virus capsids
Seminar Room 2, Newton Institute Gatehouse
A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries: T1, T2, T3, pT3, T4, and T7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the Calpha atoms. The number of these atoms ranges between 8460 (for SPMV -- satellite panicum mosaic virus) and 135780 (for NBV -- nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic F_c results in a drop in the force and emergence of irreversibility. Across the 35 capsids studied, both F_c and the elastic constant are observed to vary by a factor of 20. We argue that for a given linear size of the capsid the elastic constant and F_c depend on the average coordination number of an amino acid in the capsid.